- EMDB-11621: Class 4 of three-dimensional classification of single asymmetric ... -
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基本情報
登録情報
データベース: EMDB / ID: EMD-11621
タイトル
Class 4 of three-dimensional classification of single asymmetric units of RV-A89 into six classes. The class averages reveal differences at the RNA/protein interfaces.
マップデータ
Class 4 of three-dimensional classification of single asymmetric units of RV-A89 into six classes. The class averages reveal differences at the RNA/protein interfaces.
ジャーナル: Commun Biol / 年: 2020 タイトル: Individual subunits of a rhinovirus causing common cold exhibit largely different protein-RNA contact site conformations. 著者: Dieter Blaas / 要旨: Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA ...Rhinoviruses cause the common cold. They are icosahedral, built from sixty copies each of the capsid proteins VP1 through VP4 arranged in a pseudo T = 3 lattice. This shell encases a ss(+) RNA genome. Three-D classification of single and oligomeric asymmetric units computationally excised from a 2.9 Å cryo-EM density map of rhinovirus A89, showed that VP4 and the N-terminal extension of VP1 adopt different conformations within the otherwise identical 3D-structures. Analysis of up to sixty classes of single subunits and of six classes of subunit dimers, trimers, and pentamers revealed different orientations of the amino acid residues at the interface with the RNA suggesting that local asymmetry is dictated by disparities of the interacting nucleotide sequences. The different conformations escape detection by 3-D structure determination of entire virions with the conformational heterogeneity being only indicated by low density. My results do not exclude that the RNA follows a conserved assembly mechanism, contacting most or all asymmetric units in a specific way. However, as suggested by the gradual loss of asymmetry with increasing oligomerization and the 3D-structure of entire virions reconstructed by using Euler angles selected in the classification of single subunits, RNA path and/or folding likely differ from virion to virion.
#20 - 2001年8月 ポリオウイルスとライノウイルス (Poliovirus and Rhinovirus) 類似性 (1)
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マップ
ファイル
ダウンロード / ファイル: emd_11621.map.gz / 形式: CCP4 / 大きさ: 347.6 MB / タイプ: IMAGE STORED AS FLOATING POINT NUMBER (4 BYTES)
注釈
Class 4 of three-dimensional classification of single asymmetric units of RV-A89 into six classes. The class averages reveal differences at the RNA/protein interfaces.
ボクセルのサイズ
X=Y=Z: 0.97 Å
密度
表面レベル
登録者による: 0.002 / ムービー #1: 0.002
最小 - 最大
-0.011815332 - 0.018784637
平均 (標準偏差)
0.0000088368 (±0.00030056562)
対称性
空間群: 1
詳細
EMDB XML:
マップ形状
Axis order
X
Y
Z
Origin
0
0
0
サイズ
450
450
450
Spacing
450
450
450
セル
A=B=C: 436.5 Å α=β=γ: 90.0 °
CCP4マップ ヘッダ情報:
mode
Image stored as Reals
Å/pix. X/Y/Z
0.97
0.97
0.97
M x/y/z
450
450
450
origin x/y/z
0.000
0.000
0.000
length x/y/z
436.500
436.500
436.500
α/β/γ
90.000
90.000
90.000
start NX/NY/NZ
0
0
0
NX/NY/NZ
161
186
271
MAP C/R/S
1
2
3
start NC/NR/NS
0
0
0
NC/NR/NS
450
450
450
D min/max/mean
-0.012
0.019
0.000
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添付データ
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試料の構成要素
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全体 : Rhinovirus A
全体
名称: Rhinovirus A (ライノウイルス)
要素
ウイルス: Rhinovirus A (ライノウイルス)
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超分子 #1: Rhinovirus A
超分子
名称: Rhinovirus A / タイプ: virus / ID: 1 / 親要素: 0 / NCBI-ID: 147711 / 生物種: Rhinovirus A / Sci species strain: Rhinovirus A89 / ウイルスタイプ: VIRION / ウイルス・単離状態: SEROTYPE / ウイルス・エンベロープ: No / ウイルス・中空状態: No